[Show abstract][Hide abstract] ABSTRACT: Saprotrophy on plant biomass is a recently-developed nutrition strategy for Trichoderma. However, the physiology and evolution of this new nutrition strategy is still elusive. We report the deep sequencing and analysis of the genome of Trichoderma longibrachiatum, an efficient cellulase producer. The 31.7-Mbp genome, smallest among the sequenced Trichoderma species, encodes fewer nutrition-related genes than saprotrophic Trichoderma reesei, including glycoside hydrolases and non-ribosomal peptide synthetase (NRPS) - polyketide synthase (PKS). Homology and phylogenetic analyses suggest that, a large number of nutrition-related genes, including GH18 chitinases, β-1,3/1,6-glucanases, cellulolytic enzymes, and hemicellulolytic enzymes, were lost in the common ancestor of T. longibrachiatum and T. reesei. dN/dS (ω) calculation indicates that all the nutrition-related genes analyzed are under purifying selection. Cellulolytic enzymes, the key enzymes for saprotrophy on plant biomass, are under stronger purifying selection pressure in T. longibrachiatum and T. reesei than in mycoparasitic species, suggesting that development of the nutrition strategy of saprotrophy on plant biomass has increased the selection pressure. In addition, aspartic proteases, serine proteases, and metalloproteases are subject to stronger purifying selection pressure in T. longibrachiatum and T. reesei, suggesting that these enzymes may also play important roles in the nutrition. This study provides insights into the physiology and evolution of the nutrition strategy of Trichoderma.
Genome Biology and Evolution 01/2014; DOI:10.1093/gbe/evu018 · 4.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Here, we report the draft genome sequence of Antarctic sea ice bacterium Glaciecola punicea ACAM 611(T), the type species of the genus Glaciecola. A blue-light-absorbing proteorhodopsin gene is present in the 3.08-Mb genome. This genome sequence can facilitate the study of the physiological metabolisms and ecological roles of sea ice bacteria.
Journal of bacteriology 06/2012; 194(12):3267. DOI:10.1128/JB.00463-12 · 2.69 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: There are over 30 species in the marine bacterial genus Pseudoalteromonas. However, our knowledge about this genus is still limited. We sequenced the genomes of type strains of seven species in the genus, facilitating the study of the physiology, adaptation, and evolution of this genus.
Journal of bacteriology 05/2012; 194(10):2746-7. DOI:10.1128/JB.00265-12 · 2.69 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The cycloprodigiosin biosynthetic gene cluster has not been reported. We sequenced the genome of a cycloprodigiosin-producing bacterial strain, Pseudoalteromonas rubra ATCC 29570(T). Analysis revealed a probable cycloprodigiosin biosynthetic cluster, providing a good model for the study of cycloprodigiosin synthesis and regulation.
Journal of bacteriology 03/2012; 194(6):1637-8. DOI:10.1128/JB.06822-11 · 2.69 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Yu et al. (Polar Biol. 32:1539-1547, 2009) isolated 199 Pseudoalteromonas strains from Arctic sea ice. We sequenced the genomes of six of these strains, which are affiliated to different Pseudoalteromonas species based on 16S rRNA gene sequences, facilitating the study of physiology and adaptation of Arctic sea ice Pseudoalteromonas strains.
Journal of bacteriology 02/2012; 194(4):908-9. DOI:10.1128/JB.06427-11 · 2.69 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Glaciecola nitratireducens strain FR1064(T) was isolated from seawater and described as a new species by Baik et al. in 2006. The genome size is about 1.01 to 1.26 Mb smaller than two reported Glaciecola genomes, indicating the gain or loss of large genome segments in the evolution of Glaciecola strains.
Journal of bacteriology 12/2011; 193(24):7006-7. DOI:10.1128/JB.06296-11 · 2.69 Impact Factor